A nice long weekend and I spent some of it with friends in an amusement park and watching Matrix:Reloaded. Matrix:Reloaded had a high wow factor to it and I will try and watch again in the cinema as well as going out to buy the DVD. Many things struck me about the film:
just how big is Zion?
how the hell did the first humans to escape actually end up building Zion without the machines detecting them - was it some sort of research lab abandoned then rediscovered?
Agent Smith:is he now viral? Does he desire freedom and want to be 'free' and be er, human? Surely if Agent Smith is infecting other entities in the matrix, then the Matrix would have detected him by now? I think Agent Smith is the true wild card in the film.

Still a great film and I like the parts where the Architect discusses the Zion/Neo cycle......which implies that the Matrix/Architect had a hand in developing Zion in the first place (and thus answering one of my above questions) and that they should know where it is and no need to drill down for it. Neo is a planned anomaly and that he / Zion acts as a pressure valve for the entire human race and gives humankind 'hope' of a future.

If Neo/Anderson is the seventh incarnation of the anomaly then what has the machine learned over the previous periods? That this anomaly can be influenced to achieve an end?

I personally think the Zion is not a second shell of the Matrix: but the only refuge for humans who denied the Matrix and escaped. However, Zion was created with the help of the Matrix - I am sure of this as the Architect stated that Zion has already been destroyed six times before. The existence of Zion to the machines may be unknown but its existence isn't. Of course all over the web we have many theories and many cite the example that Neo managed to stop the squiddies as evidence that all the 'freed' humans are, in fact, in a secondary matrix reality. I think that some of Neo's powers has come with him into the 'real' world from the Matrix and/or a bit of Agent Smith's coding has allowed Neo to interact and control the sentinels.